Investigating einkorn domestication using phylogenetic networks

The transition from hunting-gathering to agriculture began 10,000 years ago in the Fertile Crescent, an area covering parts of present day Egypt, Gaza Strip, Iran, Iraq, Israel, Jordan, Lebanon, Syria, Turkey and West Bank. A number of founder crops are believed to have originated here including einkorn, emmer and barley. Much work has been conducted to investigate the origins of agriculture, however the mechanisms by which morphologically distinct domesticated crops were produced from cultivated progenitors is not yet fully understood.AFLPs and Neighbor-Joining trees have been used to explore the relationships between wild and domesticated crops which invariably produce trees that appear monophyletic, often in contrast to archaeological evidence. Simulations of AFLP evolution and analysis by Neighbor-Joining indicated that populations often appear to be monophyletic even if derived from multiple populations. These simulations, combined with the conflicting archaeological evidence suggest that AFLPs and Neighbor-Joining might not be a suitable approach when investigating the origins of agriculture.As an alternative we are using einkorn 5S spacer sequences to construct phylogenetic networks. Einkorn wheat has been chosen as a species which was domesticated in the Fertile Crescent but has had little agricultural use in the last 5000 years; as such modern domesticated einkorn will not have been through additional bottlenecks caused by modern agricultural intensive breeding. The 5S-DNA-A1 array consists of repeating 5S ribosomal gene and spacer units and is known to evolve rapidly, a property which is essential when looking at such recent evolutionary timescales. A disadvantage however is that the array evolves in a concerted fashion, with homogenisation processes which create reticulate relationships between sequences. For this reason we require phylogenetic networks rather than trees to depict these relationships. We use pruned quasi-median networks which retain shortest paths between pairs of sequences in the network, where the shortest path is equivalent to the minimum number of steps required to convert one sequence to the other.The wild einkorn samples are from Turkey, Syria, Iraq and Iran. We are in the process of generating thousands of 5S spacer sequences from these samples to investigate the variation within an individual and within a population. Analysis of the networks produced from single seeds has revealed the majority of sequences are contained within large consensus nodes with few duplicated non-consensus sequences. Comparisons of seeds from different geographic regions has provided insights into the relationships between different einkorn populations within the Fertile Crescent.